I started a project on my Sam440 but needed to continue the project using my iBook running MorphOS however when transfering files using a flash drive I ended up with corrupt files, extra folders or item events missing.

Is there a reason for this and if so can the projects be transferred a different way?

Transferring projects should actually be really easy and convenient because Designer forces you to store all files that belong to your project in the same directory so you can just copy the whole project directory to somewhere else and it should work out of the box. Which error do you get?